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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ), 'gf_id' => 'HOM05D001961', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001961' ), 'data_identifier' => 'HOM05D001961', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001961', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p25750' => 'bna', 'A06p19710' => 'bna', 'A06p19720' => 'bna', 'A06p19750' => 'bna', 'Aa31LG11G1000' => 'aar', 'Aa31LG4G16560' => 'aar', 'Actinidia04931' => 'ach', 'Actinidia06060' => 'ach', 'Actinidia06064' => 'ach', 'Actinidia09230' => 'ach', 'Actinidia09231' => 'ach', 'Actinidia33021' => 'ach', 'Actinidia34975' => 'ach', 'Actinidia36031' => 'ach', 'Actinidia36032' => 'ach', 'Actinidia36035' => 'ach', 'Actinidia36036' => 'ach', 'Actinidia37046' => 'ach', 'Actinidia37183' => 'ach', 'Actinidia37665' => 'ach', 'Actinidia37666' => 'ach', 'Ah.02g113120' => 'amhyb', 'Ah.02g120940' => 'amhyb', 'Ah.02g120980' => 'amhyb', 'Ah.11g048820' => 'amhyb', 'Ah.11g048830' => 'amhyb', 'AL5G27220' => 'aly', 'AL5G27230' => 'aly', 'Aqoxy2G03120' => 'aox', 'Aqoxy3G00721' => 'aox', 'Aqoxy3G00811' => 'aox', 'Aqoxy3G03236' => 'aox', 'Aqoxy4G02898' => 'aox', 'Aqoxy4G02899' => 'aox', 'Aqoxy4G02900' => 'aox', 'Aqoxy4G02905' => 'aox', 'Aqoxy4G02906' => 'aox', 'Aqoxy4G02909' => 'aox', 'Aqoxy4G02934' => 'aox', 'Aqoxy4G02935' => 'aox', 'Aqoxy4G02940' => 'aox', 'Aqoxy5G01466' => 'aox', 'Aqoxy6G01672' => 'aox', 'Aqoxy6G02946' => 'aox', 'arahy.Tifrunner.gnm1.ann1.DV6TYS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LMB17M' => 'arhy', 'AT3G47890' => 'ath', 'AT3G47910' => 'ath', 'ATR1153G111' => 'atr', 'Atru.chr8.2435' => 'acertr', 'Atru.chr8.2437' => 'acertr', 'Atru.chr9.2337' => 'acertr', 'AUR62008343' => 'cqu', 'AUR62021754' => 'cqu', 'BcaB01g00864' => 'bca', 'BcaB01g00865' => 'bca', 'BcaB01g00866' => 'bca', 'BcaB02g10685' => 'bca', 'BcaB05g23091' => 'bca', 'BcaC01g01759' => 'bca', 'BcaC01g01766' => 'bca', 'BcaC03g16564' => 'bca', 'BcaC09g49829' => 'bca', 'BolC1t03187H' => 'bol', 'BolC1t03189H' => 'bol', 'BolC3t19509H' => 'bol', 'BolC3t19510H' => 'bol', 'BolC3t19515H' => 'bol', 'BraA01t02491Z' => 'bra', 'BraA06t25050Z' => 'bra', 'BraA06t25054Z' => 'bra', 'C01p32520' => 'bna', 'C01p32530' => 'bna', 'C02p43790' => 'bna', 'C03p72130' => 'bna', 'C03p72140' => 'bna', 'C03p72190' => 'bna', 'CAN.G628.49' => 'can', 'CAN.G999.31' => 'can', 'CANSAT78G2446' => 'cansat', 'CANSAT80G1878' => 'cansat', 'CARHR156620' => 'chi', 'CARHR156630' => 'chi', 'Carub.0005s1403' => 'cru', 'Carub.0005s1404' => 'cru', 'Ca_21858_v3' => 'car', 'CBR_g34786' => 'cbr', 'Cc04_g15870' => 'ccan', 'Cc04_g15890' => 'ccan', 'Cc04_g15900' => 'ccan', 'Cc06_g20580' => 'ccan', 'Cc06_g20590' => 'ccan', 'CDE06G0073' => 'cde', 'CDE06G2189' => 'cde', 'CDE07G1845' => 'cde', 'Cfa000802' => 'cfa', 'Cfa009757' => 'cfa', 'Cfa009758' => 'cfa', 'Cfa009760' => 'cfa', 'Cfa009789' => 'cfa', 'Cfa009799' => 'cfa', 'Cfa009800' => 'cfa', 'Cfa009801' => 'cfa', 'Cfa009804' => 'cfa', 'Cfa017823' => 'cfa', 'Cfa019014' => 'cfa', 'Cfa021166' => 'cfa', 'Ciclev10007036m.g' => 'ccl', 'Ciclev10013440m.g' => 'ccl', 'Ciclev10018472m.g' => 'ccl', 'Ciclev10018876m.g' => 'ccl', 'Ciclev10024647m.g' => 'ccl', 'CiPaw.11G036500' => 'cil', 'CiPaw.13G162000' => 'cil', 'CiPaw.14G120700' => 'cil', 'ClCG06G016460' => 'cla', 'COL.COLO4_32730' => 'col', 'COL.COLO4_35465' => 'col', 'Cpa.g.sc17.186' => 'cpa', 'Cre12.g508250' => 'cre', 'Cre16.g670850' => 'cre', 'CsaV3_1G002070' => 'csa', 'CSS0004686' => 'camsi', 'CSS0012336' => 'camsi', 'CSS0014551' => 'camsi', 'CSS0026536' => 'camsi', 'CSS0030881' => 'camsi', 'CSS0034267' => 'camsi', 'CSS0037638' => 'camsi', 'CSS0044384' => 'camsi', 'CSS0045618' => 'camsi', 'CSS0045619' => 'camsi', 'DCAR_021541' => 'dca', 'DCAR_026083' => 'dca', 'Dinv17123' => 'din', 'Dinv19903' => 'din', 'Dinv33700' => 'din', 'Dinv33701' => 'din', 'Dinv33702' => 'din', 'Dinv33704' => 'din', 'Dinv33705' => 'din', 'Dinv33706' => 'din', 'Dinv33707' => 'din', 'Dinv33708' => 'din', 'Dinv33709' => 'din', 'Dinv33730' => 'din', 'Dinv38651' => 'din', 'Duzib068G1318' => 'dzi', 'Duzib205G1945' => 'dzi', 'ECA246G4653' => 'eca', 'EL10Ac5g10921' => 'bvu', 'Eucgr.B00398' => 'egr', 'Eucgr.K02911' => 'egr', 'FAN04G1134' => 'fan', 'FAN08G2604' => 'fan', 'FAN13G0464' => 'fan', 'FAN18G4418' => 'fan', 'FvH4_5g15740' => 'fve', 'Glyma.05G031000' => 'gma', 'Glyma.17G095800' => 'gma', 'Gohir.A03G064400' => 'ghi', 'Gohir.A11G028810' => 'ghi', 'Gohir.D03G090700' => 'ghi', 'Gohir.D11G032100' => 'ghi', 'Gorai.003G070500' => 'gra', 'Gorai.007G034900' => 'gra', 'GSVIVG01008079001' => 'vvi', 'GSVIVG01032594001' => 'vvi', 'GSVIVG01032595001' => 'vvi', 'HanXRQChr05g0155261' => 'han', 'HanXRQChr08g0236941' => 'han', 'Haze_05891' => 'cav', 'Haze_05892' => 'cav', 'Haze_05893' => 'cav', 'Haze_05896' => 'cav', 'Haze_05897' => 'cav', 'Haze_06878' => 'cav', 'Haze_07394' => 'cav', 'Haze_23122' => 'cav', 'Haze_23124' => 'cav', 'Haze_23167' => 'cav', 'Haze_23170' => 'cav', 'Hma1.2p1_0002F.1_g003390' => 'hma', 'Hma1.2p1_0002F.1_g003400' => 'hma', 'Hma1.2p1_0104F.1_g050400' => 'hma', 'HPP92_023510' => 'vpl', 'HPP92_023511' => 'vpl', 'HPP92_023554' => 'vpl', 'HPP92_023555' => 'vpl', 'HPP92_023556' => 'vpl', 'Hund02679' => 'sun', 'Hund09373' => 'sun', 'Lalb_Chr12g0201211' => 'lal', 'Lalb_Chr13g0298141' => 'lal', 'Lj1g0021908' => 'lja', 'Lj4g0028007' => 'lja', 'Lj5C117T8' => 'lonja', 'Lj9C457G12' => 'lonja', 'Lsat_1_v5_gn_1_11560' => 'lsa', 'Lsat_1_v5_gn_5_18460' => 'lsa', 'Lsat_1_v5_gn_8_134260' => 'lsa', 'Manes.06G097300' => 'mes', 'Manes.14G073702' => 'mes', 'MBI01_g01232_MAGBIO' => 'mbi', 'MBI04_g20664_MAGBIO' => 'mbi', 'MBI04_g20665_MAGBIO' => 'mbi', 'MBI04_g20667_MAGBIO' => 'mbi', 'MBI04_g20668_MAGBIO' => 'mbi', 'MBI04_g20669_MAGBIO' => 'mbi', 'MBI05_g43547_MAGBIO' => 'mbi', 'MBI05_g43548_MAGBIO' => 'mbi', 'MBI11_g41494_MAGBIO' => 'mbi', 'MBI17_g34065_MAGBIO' => 'mbi', 'MCO16G562' => 'mco', 'MD06G1185800' => 'mdo', 'MD14G1192000' => 'mdo', 'Medtr4g107470' => 'mtr', 'MELO3C017148.2' => 'cme', 'Migut.I00114' => 'egut', 'Migut.I00115' => 'egut', 'MSTRG.11404' => 'ama', 'Nitab4.5_0000003g0050' => 'nta', 'Nitab4.5_0000909g0070' => 'nta', 'Nitab4.5_0004478g0040' => 'nta', 'Nitab4.5_0007282g0070' => 'nta', 'Nn1g04369' => 'nnu', 'Nn3g17102' => 'nnu', 'Nn4g23006' => 'nnu', 'Oeu006169.1' => 'oeu', 'Oeu006172.1' => 'oeu', 'Oeu006173.1' => 'oeu', 'Oeu020375.1' => 'oeu', 'Oeu022619.1' => 'oeu', 'Oeu022639.1' => 'oeu', 'Oeu039544.2' => 'oeu', 'Os03g0165600' => 'osa', 'Peaxi162Scf00009g00524' => 'pax', 'Peaxi162Scf00689g00564' => 'pax', 'PGR083G2262' => 'pgr', 'PGSC0003DMG400013181' => 'stu', 'PGSC0003DMG400033067' => 'stu', 'Phvul.003G194200' => 'pvu', 'Potri.012G071900' => 'ptr', 'Potri.015G066500' => 'ptr', 'Potri.017G089250' => 'ptr', 'Pp3c16_3030' => 'ppa', 'Pp3c27_3670' => 'ppa', 'PRCOL_00004010' => 'pco', 'Prupe.5G184600' => 'ppe', 'Psat3g053360' => 'psa', 'Psat4g054160' => 'psa', 'Psat6g087520' => 'psa', 'Psat7g159040' => 'psa', 'PSO161G0006' => 'pso', 'PSO161G0075' => 'pso', 'PSO161G0094' => 'pso', 'PSO210G2491' => 'pso', 'PSO210G7105' => 'pso', 'PSO478G3093' => 'pso', 'PSO478G4671' => 'pso', 'PSO541G1898' => 'pso', 'PSO541G4677' => 'pso', 'PSO591G0439' => 'pso', 'PSO832G1192' => 'pso', 'QL05p014721' => 'qlo', 'QL05p014726' => 'qlo', 'QL05p015524' => 'qlo', 'QL05p015531' => 'qlo', 'QL05p015549' => 'qlo', 'QL05p015555' => 'qlo', 'QL05p016130' => 'qlo', 'QL05p016138' => 'qlo', 'QL05p016151' => 'qlo', 'QL05p016244' => 'qlo', 'QL05p016288' => 'qlo', 'QL05p016300' => 'qlo', 'QL05p016329' => 'qlo', 'QL05p016885' => 'qlo', 'QL05p016906' => 'qlo', 'QL05p016929' => 'qlo', 'QL05p016939' => 'qlo', 'QL05p016944' => 'qlo', 'QL05p016954' => 'qlo', 'QL05p016973' => 'qlo', 'QL05p016983' => 'qlo', 'QL05p017027' => 'qlo', 'QL05p017038' => 'qlo', 'QL05p017074' => 'qlo', 'QL05p017088' => 'qlo', 'QL05p032445' => 'qlo', 'QL10p014874' => 'qlo', 'QL10p014886' => 'qlo', 'RcHm_v2.0_Chr7g0180371' => 'rch', 'Rhsim08G0161300' => 'rsi', 'Rhsim10G0031400' => 'rsi', 'Rhsim10G0032100' => 'rsi', 'Sabra12G0051100' => 'sbr', 'Sabra12G0051300' => 'sbr', 'Sabra15G0091600' => 'sbr', 'Sabra16G0071600' => 'sbr', 'Sabra16G0071800' => 'sbr', 'Sabra16G0073700' => 'sbr', 'Sabra17G0078800' => 'sbr', 'SalBow5G1786' => 'sbo', 'SalBow7G0691' => 'sbo', 'Sc04g0002330' => 'sci', 'Sed0025522' => 'sed', 'SEGI_13866' => 'sgi', 'SGA_v2.0_scaffold114G31883' => 'sas', 'SGA_v2.0_scaffold4G02083' => 'sas', 'SGA_v2.0_scaffold7G04090' => 'sas', 'Solyc03g113370.3' => 'sly', 'Solyc06g071120.3' => 'sly', 'Solyc10g050055.1' => 'sly', 'Sopen03g032420' => 'spe', 'Sopen06g027420' => 'spe', 'Sopen10g021180' => 'spe', 'Sp5g14040' => 'spa', 'Sp5g14050' => 'spa', 'TAR374G1240' => 'tar', 'TAR622G0827' => 'tar', 'THA.LOC104821450' => 'tha', 'Thecc.03G077100' => 'tca', 'Thhalv10010059m.g' => 'esa', 'Thhalv10010060m.g' => 'esa', 'TPR.G38388' => 'tpr', 'TWI15G0443' => 'twi', 'TWI60G1556' => 'twi', 'TWI63G1535' => 'twi', 'TWI81G0197' => 'twi', 'TWI81G0306' => 'twi', 'unitig_744.g24389' => 'ugi', 'vmacro05744' => 'vma', 'vmacro19421' => 'vma', 'VMungo1215G0372' => 'vmu', 'Zm00001eb005070' => 'zma', 'Zm00001eb403430' => 'zma' ) $gf_id = 'HOM05D001961' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001961' ) $data_identifier = 'HOM05D001961' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 15, 'amhyb' => (int) 5, 'aly' => (int) 2, 'aox' => (int) 16, 'arhy' => (int) 2, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 3, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 1, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 12, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 2, 'cpa' => (int) 1, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 10, 'dca' => (int) 2, 'din' => (int) 13, 'dzi' => (int) 2, 'eca' => (int) 1, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 3, 'han' => (int) 2, 'cav' => (int) 11, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 2, 'lja' => (int) 2, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 2, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 2, 'mtr' => (int) 1, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 1, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 28, 'rch' => (int) 1, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 1, 'sas' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 2, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 2, 'tpr' => (int) 1, 'twi' => (int) 5, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 1, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403430' $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